Multiple sequence alignment - TraesCS5B01G023700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G023700 chr5B 100.000 4202 0 0 1 4202 21752802 21748601 0.000000e+00 7760
1 TraesCS5B01G023700 chr5B 94.378 249 14 0 2736 2984 21727746 21727994 2.370000e-102 383
2 TraesCS5B01G023700 chr5B 87.356 87 10 1 3797 3883 21729372 21729457 9.610000e-17 99
3 TraesCS5B01G023700 chr5D 94.683 3686 135 18 1 3667 30118857 30115214 0.000000e+00 5664
4 TraesCS5B01G023700 chr5D 88.276 1143 70 29 2542 3625 29902215 29901078 0.000000e+00 1310
5 TraesCS5B01G023700 chr5D 89.036 830 47 16 2542 3367 29879159 29879948 0.000000e+00 989
6 TraesCS5B01G023700 chr5D 91.129 248 17 5 3090 3334 30112194 30111949 8.710000e-87 331
7 TraesCS5B01G023700 chr5D 90.283 247 16 2 3739 3984 29900919 29900680 2.440000e-82 316
8 TraesCS5B01G023700 chr5D 93.567 171 10 1 3835 4004 30114767 30114597 1.940000e-63 254
9 TraesCS5B01G023700 chr5D 93.750 80 5 0 3663 3742 492282472 492282551 2.050000e-23 121
10 TraesCS5B01G023700 chr2B 92.941 85 4 2 3667 3751 782755536 782755454 5.710000e-24 122
11 TraesCS5B01G023700 chr7D 92.771 83 6 0 3667 3749 616006616 616006534 2.050000e-23 121
12 TraesCS5B01G023700 chr7D 90.909 88 6 2 3667 3753 350149406 350149320 2.650000e-22 117
13 TraesCS5B01G023700 chr4A 91.111 90 6 2 3664 3751 735658263 735658174 2.050000e-23 121
14 TraesCS5B01G023700 chr4A 91.765 85 6 1 3670 3754 683881238 683881155 2.650000e-22 117
15 TraesCS5B01G023700 chr3A 93.750 80 5 0 3663 3742 739385338 739385259 2.050000e-23 121
16 TraesCS5B01G023700 chr3A 94.737 76 4 0 3667 3742 391475400 391475475 7.380000e-23 119
17 TraesCS5B01G023700 chr1B 93.750 80 5 0 3663 3742 597465152 597465231 2.050000e-23 121


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G023700 chr5B 21748601 21752802 4201 True 7760 7760 100.000000 1 4202 1 chr5B.!!$R1 4201
1 TraesCS5B01G023700 chr5B 21727746 21729457 1711 False 241 383 90.867000 2736 3883 2 chr5B.!!$F1 1147
2 TraesCS5B01G023700 chr5D 30111949 30118857 6908 True 2083 5664 93.126333 1 4004 3 chr5D.!!$R2 4003
3 TraesCS5B01G023700 chr5D 29879159 29879948 789 False 989 989 89.036000 2542 3367 1 chr5D.!!$F1 825
4 TraesCS5B01G023700 chr5D 29900680 29902215 1535 True 813 1310 89.279500 2542 3984 2 chr5D.!!$R1 1442

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
775 785 0.617413 AGTTGGATCAGGCACTCTGG 59.383 55.000 0.00 0.0 43.53 3.86 F
1212 1222 0.695347 AAGAACCTTCTCCCTGCCAG 59.305 55.000 0.00 0.0 36.28 4.85 F
2380 2390 1.076024 ACTGGCAGACCCAATGTTGAT 59.924 47.619 23.66 0.0 44.81 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 1601 0.042131 TTCCCCGGGTAGTGATGACT 59.958 55.0 21.85 0.0 36.07 3.41 R
2476 2486 0.322456 TGCACCCAGTGGCATAGTTC 60.322 55.0 2.61 0.0 34.58 3.01 R
4027 5299 0.108138 GTGGCCGATCTTGCAGTAGT 60.108 55.0 0.00 0.0 0.00 2.73 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 3.552890 CGCATCTTAACCCAGATCGATGA 60.553 47.826 0.54 0.00 30.50 2.92
56 57 4.310769 CATCTTAACCCAGATCGATGACC 58.689 47.826 0.54 0.00 30.50 4.02
67 68 2.014335 TCGATGACCATGTTCTGCTG 57.986 50.000 0.00 0.00 0.00 4.41
72 73 2.221169 TGACCATGTTCTGCTGTTGTC 58.779 47.619 0.00 0.00 0.00 3.18
75 76 3.668447 ACCATGTTCTGCTGTTGTCTAG 58.332 45.455 0.00 0.00 0.00 2.43
77 78 3.434641 CCATGTTCTGCTGTTGTCTAGTG 59.565 47.826 0.00 0.00 0.00 2.74
78 79 2.483876 TGTTCTGCTGTTGTCTAGTGC 58.516 47.619 0.00 0.00 0.00 4.40
79 80 2.103094 TGTTCTGCTGTTGTCTAGTGCT 59.897 45.455 0.00 0.00 0.00 4.40
80 81 3.320826 TGTTCTGCTGTTGTCTAGTGCTA 59.679 43.478 0.00 0.00 0.00 3.49
81 82 3.857549 TCTGCTGTTGTCTAGTGCTAG 57.142 47.619 0.00 0.00 34.56 3.42
82 83 3.157881 TCTGCTGTTGTCTAGTGCTAGT 58.842 45.455 6.18 0.00 34.84 2.57
83 84 3.574396 TCTGCTGTTGTCTAGTGCTAGTT 59.426 43.478 6.18 0.00 34.84 2.24
84 85 4.039245 TCTGCTGTTGTCTAGTGCTAGTTT 59.961 41.667 6.18 0.00 34.84 2.66
85 86 4.307432 TGCTGTTGTCTAGTGCTAGTTTC 58.693 43.478 6.18 0.84 34.84 2.78
86 87 4.039245 TGCTGTTGTCTAGTGCTAGTTTCT 59.961 41.667 6.18 0.00 34.84 2.52
87 88 4.991687 GCTGTTGTCTAGTGCTAGTTTCTT 59.008 41.667 6.18 0.00 34.84 2.52
88 89 5.467063 GCTGTTGTCTAGTGCTAGTTTCTTT 59.533 40.000 6.18 0.00 34.84 2.52
89 90 6.017852 GCTGTTGTCTAGTGCTAGTTTCTTTT 60.018 38.462 6.18 0.00 34.84 2.27
90 91 7.478520 TGTTGTCTAGTGCTAGTTTCTTTTC 57.521 36.000 6.18 0.00 34.84 2.29
93 94 8.613482 GTTGTCTAGTGCTAGTTTCTTTTCTTT 58.387 33.333 6.18 0.00 34.84 2.52
114 115 5.772825 TTTTTGTCTCACTCCCTCATTTG 57.227 39.130 0.00 0.00 0.00 2.32
140 141 7.862512 AGATCAGTCCAAGATCTCAAAATTC 57.137 36.000 0.00 0.00 46.97 2.17
145 146 2.223340 CCAAGATCTCAAAATTCGGCCG 60.223 50.000 22.12 22.12 0.00 6.13
169 170 4.514781 TCGTAAGATCCACCGATATTGG 57.485 45.455 7.52 7.52 45.01 3.16
171 172 2.568623 AAGATCCACCGATATTGGCC 57.431 50.000 9.11 0.00 33.71 5.36
173 174 0.673644 GATCCACCGATATTGGCCCG 60.674 60.000 9.11 0.00 33.71 6.13
175 176 2.978010 CACCGATATTGGCCCGGC 60.978 66.667 16.24 0.00 46.54 6.13
204 205 3.555966 ACCAAGTTTTAGCTGCTTGAGT 58.444 40.909 7.79 12.82 41.31 3.41
214 215 3.539604 AGCTGCTTGAGTATGCTTTAGG 58.460 45.455 0.00 0.00 0.00 2.69
223 224 5.611374 TGAGTATGCTTTAGGGATAGTTGC 58.389 41.667 0.00 0.00 33.07 4.17
233 234 1.369091 GGATAGTTGCTGGCACGTGG 61.369 60.000 18.88 1.27 0.00 4.94
261 262 5.673337 CAGATGTGGAAAAACGAAGAAGA 57.327 39.130 0.00 0.00 0.00 2.87
262 263 5.444122 CAGATGTGGAAAAACGAAGAAGAC 58.556 41.667 0.00 0.00 0.00 3.01
263 264 5.007626 CAGATGTGGAAAAACGAAGAAGACA 59.992 40.000 0.00 0.00 0.00 3.41
264 265 5.588648 AGATGTGGAAAAACGAAGAAGACAA 59.411 36.000 0.00 0.00 0.00 3.18
265 266 5.630661 TGTGGAAAAACGAAGAAGACAAA 57.369 34.783 0.00 0.00 0.00 2.83
266 267 6.202516 TGTGGAAAAACGAAGAAGACAAAT 57.797 33.333 0.00 0.00 0.00 2.32
267 268 7.323049 TGTGGAAAAACGAAGAAGACAAATA 57.677 32.000 0.00 0.00 0.00 1.40
268 269 7.763356 TGTGGAAAAACGAAGAAGACAAATAA 58.237 30.769 0.00 0.00 0.00 1.40
269 270 7.698970 TGTGGAAAAACGAAGAAGACAAATAAC 59.301 33.333 0.00 0.00 0.00 1.89
270 271 7.913821 GTGGAAAAACGAAGAAGACAAATAACT 59.086 33.333 0.00 0.00 0.00 2.24
271 272 9.111613 TGGAAAAACGAAGAAGACAAATAACTA 57.888 29.630 0.00 0.00 0.00 2.24
272 273 9.595357 GGAAAAACGAAGAAGACAAATAACTAG 57.405 33.333 0.00 0.00 0.00 2.57
273 274 9.595357 GAAAAACGAAGAAGACAAATAACTAGG 57.405 33.333 0.00 0.00 0.00 3.02
312 313 3.450457 AGCAGGTTCAGATCTTGGTCTAG 59.550 47.826 0.00 0.00 0.00 2.43
385 386 7.029563 GTCTGTTATCCATTGTTTTCCATGAC 58.970 38.462 0.00 0.00 0.00 3.06
393 394 3.576078 TGTTTTCCATGACCTGTCAGT 57.424 42.857 6.13 0.00 43.61 3.41
411 412 7.759433 CCTGTCAGTGAAAATGTTTTTACAGTT 59.241 33.333 13.37 0.00 38.62 3.16
456 457 8.049117 TGGTTTGATAGGATAGCATGAATATCC 58.951 37.037 21.47 21.47 46.19 2.59
475 476 5.695851 ATCCAAATTTACCTCGATGCATC 57.304 39.130 17.10 17.10 0.00 3.91
476 477 4.780815 TCCAAATTTACCTCGATGCATCT 58.219 39.130 23.73 8.20 0.00 2.90
491 492 0.987294 CATCTCTCCCCTGTGTGGTT 59.013 55.000 0.00 0.00 0.00 3.67
513 523 1.522258 GCTTGAAAACGCATGTTGTGG 59.478 47.619 0.00 0.00 38.62 4.17
569 579 7.812648 AGTTATGCACGCTTTTGTTTTATCTA 58.187 30.769 0.00 0.00 0.00 1.98
574 584 5.228012 GCACGCTTTTGTTTTATCTAGATGC 59.772 40.000 15.79 5.73 0.00 3.91
580 590 8.526681 GCTTTTGTTTTATCTAGATGCGAAATG 58.473 33.333 15.79 9.59 0.00 2.32
583 593 7.841915 TGTTTTATCTAGATGCGAAATGACA 57.158 32.000 15.79 7.49 0.00 3.58
636 646 8.630278 TCTACTTTCAGCTTCGATATTTGTAC 57.370 34.615 0.00 0.00 0.00 2.90
637 647 8.248253 TCTACTTTCAGCTTCGATATTTGTACA 58.752 33.333 0.00 0.00 0.00 2.90
639 649 8.268850 ACTTTCAGCTTCGATATTTGTACAAT 57.731 30.769 9.56 2.67 0.00 2.71
644 654 6.195244 CAGCTTCGATATTTGTACAATTGTGC 59.805 38.462 21.42 19.93 0.00 4.57
659 669 7.489574 ACAATTGTGCGAACCAATTATTTTT 57.510 28.000 11.07 0.00 39.77 1.94
664 674 4.683781 GTGCGAACCAATTATTTTTCTGCA 59.316 37.500 0.00 0.00 0.00 4.41
677 687 6.740411 ATTTTTCTGCAGCAAACAAAAAGA 57.260 29.167 20.74 7.85 31.37 2.52
682 692 2.094494 TGCAGCAAACAAAAAGACGGAA 60.094 40.909 0.00 0.00 0.00 4.30
692 702 1.523758 AAAGACGGAATGTGCCTGTC 58.476 50.000 0.00 0.00 34.15 3.51
721 731 6.647334 TGACTGCATTTCTCCACATTTTTA 57.353 33.333 0.00 0.00 0.00 1.52
724 734 7.599621 TGACTGCATTTCTCCACATTTTTATTG 59.400 33.333 0.00 0.00 0.00 1.90
735 745 8.200024 TCCACATTTTTATTGAAATTCCCAGA 57.800 30.769 0.00 0.00 0.00 3.86
766 776 2.166459 TCGAGCTTGGTAGTTGGATCAG 59.834 50.000 0.00 0.00 0.00 2.90
769 779 1.340017 GCTTGGTAGTTGGATCAGGCA 60.340 52.381 0.00 0.00 33.35 4.75
775 785 0.617413 AGTTGGATCAGGCACTCTGG 59.383 55.000 0.00 0.00 43.53 3.86
777 787 1.067295 TTGGATCAGGCACTCTGGTT 58.933 50.000 0.00 0.00 43.53 3.67
780 790 2.027192 TGGATCAGGCACTCTGGTTTAC 60.027 50.000 0.00 0.00 43.53 2.01
790 800 4.567159 GCACTCTGGTTTACGAGAAATAGG 59.433 45.833 0.00 0.00 30.38 2.57
796 806 3.063588 GGTTTACGAGAAATAGGTGCAGC 59.936 47.826 8.11 8.11 0.00 5.25
819 829 6.157994 AGCTTCCCATTTATGTAGTGACCTTA 59.842 38.462 0.00 0.00 0.00 2.69
850 860 1.152030 TGGCCTTCCTGGTCTGTCT 60.152 57.895 3.32 0.00 42.07 3.41
851 861 1.298014 GGCCTTCCTGGTCTGTCTG 59.702 63.158 0.00 0.00 37.49 3.51
895 905 6.480524 TTGGTTCAGTTTCTCATTGTATCG 57.519 37.500 0.00 0.00 0.00 2.92
1005 1015 7.074653 ACTGTACCTTGTCTGATCCTTTTAA 57.925 36.000 0.00 0.00 0.00 1.52
1044 1054 7.875971 ACAACAGGATTTCAGAAATTACAGTC 58.124 34.615 9.84 0.00 0.00 3.51
1212 1222 0.695347 AAGAACCTTCTCCCTGCCAG 59.305 55.000 0.00 0.00 36.28 4.85
1345 1355 4.810491 ACACATGTTGACAATTCTTTTGGC 59.190 37.500 0.00 0.00 0.00 4.52
1378 1388 8.641499 TTGAATTCACCAAGAACAACATTTAC 57.359 30.769 7.89 0.00 39.49 2.01
1672 1682 2.556622 TCCGAAGTTCATTCTTTTGGCC 59.443 45.455 3.32 0.00 35.61 5.36
2165 2175 1.144708 TGGTGGCTCCAACATCAGAAA 59.855 47.619 5.68 0.00 44.12 2.52
2179 2189 4.275936 ACATCAGAAAGTTCTTCCCAAACG 59.724 41.667 0.00 0.00 34.74 3.60
2230 2240 1.283029 ACAGGATGGATTGGTGGACTG 59.717 52.381 0.00 0.00 43.62 3.51
2272 2282 5.552870 AGCAAGGAATTCCATACGAGTAT 57.447 39.130 26.22 0.00 38.89 2.12
2380 2390 1.076024 ACTGGCAGACCCAATGTTGAT 59.924 47.619 23.66 0.00 44.81 2.57
2476 2486 2.624838 GGAGCATGGGTTATTGGTGATG 59.375 50.000 0.00 0.00 0.00 3.07
2554 2564 2.457366 TCGGCTTCAAAGAAGAGGAC 57.543 50.000 10.72 0.00 0.00 3.85
2612 2622 2.716217 AGGCAATGGTAACTGCTTCTC 58.284 47.619 0.00 0.00 38.65 2.87
2614 2624 2.619074 GGCAATGGTAACTGCTTCTCCT 60.619 50.000 0.00 0.00 38.65 3.69
2713 2727 7.211966 ACTGGAAGAAACTTCTGATCATTTG 57.788 36.000 10.58 0.00 37.65 2.32
2722 2736 3.370840 TCTGATCATTTGTTCCCTGGG 57.629 47.619 6.33 6.33 0.00 4.45
2754 2768 4.082136 GTCGAGGAACTGTTGAAGGAGTAT 60.082 45.833 0.00 0.00 41.55 2.12
3045 3122 0.246635 TCACGCTAGAAGAACAGGCC 59.753 55.000 0.00 0.00 0.00 5.19
3235 3331 1.608590 ACACCAAGCACCGAAAGATTG 59.391 47.619 0.00 0.00 0.00 2.67
3268 3364 4.490743 TCGTCACAGCGATTCATTAGAAA 58.509 39.130 0.00 0.00 37.29 2.52
3269 3365 5.109210 TCGTCACAGCGATTCATTAGAAAT 58.891 37.500 0.00 0.00 37.29 2.17
3270 3366 5.005682 TCGTCACAGCGATTCATTAGAAATG 59.994 40.000 0.00 0.00 37.29 2.32
3274 3370 7.538678 GTCACAGCGATTCATTAGAAATGTTTT 59.461 33.333 0.00 0.00 37.29 2.43
3275 3371 8.726068 TCACAGCGATTCATTAGAAATGTTTTA 58.274 29.630 0.00 0.00 37.29 1.52
3276 3372 8.788813 CACAGCGATTCATTAGAAATGTTTTAC 58.211 33.333 0.00 0.00 37.29 2.01
3277 3373 7.692291 ACAGCGATTCATTAGAAATGTTTTACG 59.308 33.333 0.00 0.00 37.29 3.18
3278 3374 7.902917 CAGCGATTCATTAGAAATGTTTTACGA 59.097 33.333 0.00 0.00 37.29 3.43
3279 3375 8.612619 AGCGATTCATTAGAAATGTTTTACGAT 58.387 29.630 0.00 0.00 37.29 3.73
3280 3376 9.858247 GCGATTCATTAGAAATGTTTTACGATA 57.142 29.630 0.00 0.00 37.29 2.92
3312 4107 7.445707 AGCGTATCTCTGTTATAGATTCACAGA 59.554 37.037 4.56 4.56 43.71 3.41
3417 4231 9.886132 AGTACACTTGTATACCTTTTAATCTGG 57.114 33.333 0.00 0.00 32.54 3.86
3420 4234 9.010029 ACACTTGTATACCTTTTAATCTGGTTG 57.990 33.333 0.00 0.00 35.48 3.77
3449 4277 1.936547 GGTGATTGATCGAGCAACCTC 59.063 52.381 19.71 13.86 34.66 3.85
3493 4321 6.322712 TGGACAGGCATTTTAACTGTTTAAGT 59.677 34.615 0.00 0.00 44.79 2.24
3495 4323 7.381408 GGACAGGCATTTTAACTGTTTAAGTTC 59.619 37.037 0.00 0.00 46.60 3.01
3524 4357 1.129998 CTCTCGCTTTGCTCATTGTGG 59.870 52.381 0.00 0.00 0.00 4.17
3605 4446 2.158696 ACAGAGCAAAGAGGAAGCACTT 60.159 45.455 0.00 0.00 0.00 3.16
3667 4591 6.646240 GTGTGTACTCCGTAATGGTTTTCTTA 59.354 38.462 0.00 0.00 39.52 2.10
3668 4592 7.171337 GTGTGTACTCCGTAATGGTTTTCTTAA 59.829 37.037 0.00 0.00 39.52 1.85
3669 4593 7.714377 TGTGTACTCCGTAATGGTTTTCTTAAA 59.286 33.333 0.00 0.00 39.52 1.52
3670 4594 8.011673 GTGTACTCCGTAATGGTTTTCTTAAAC 58.988 37.037 0.00 0.00 42.34 2.01
3672 4596 9.423061 GTACTCCGTAATGGTTTTCTTAAACTA 57.577 33.333 0.00 0.00 42.61 2.24
3673 4597 8.907222 ACTCCGTAATGGTTTTCTTAAACTAA 57.093 30.769 0.00 0.00 42.61 2.24
3704 4628 8.780003 AGAGGGTTTAGAATACTAGAGTAGTGA 58.220 37.037 0.00 0.00 39.81 3.41
3705 4629 9.577222 GAGGGTTTAGAATACTAGAGTAGTGAT 57.423 37.037 0.00 0.00 39.81 3.06
3706 4630 9.577222 AGGGTTTAGAATACTAGAGTAGTGATC 57.423 37.037 0.00 0.00 39.81 2.92
3707 4631 9.577222 GGGTTTAGAATACTAGAGTAGTGATCT 57.423 37.037 0.00 3.59 39.81 2.75
3713 4637 8.776470 AGAATACTAGAGTAGTGATCTAAACGC 58.224 37.037 0.00 0.00 39.81 4.84
3714 4638 8.680039 AATACTAGAGTAGTGATCTAAACGCT 57.320 34.615 0.00 0.00 39.81 5.07
3715 4639 6.607735 ACTAGAGTAGTGATCTAAACGCTC 57.392 41.667 0.00 0.00 37.69 5.03
3716 4640 6.350906 ACTAGAGTAGTGATCTAAACGCTCT 58.649 40.000 0.00 12.65 37.69 4.09
3717 4641 6.824704 ACTAGAGTAGTGATCTAAACGCTCTT 59.175 38.462 13.02 0.80 37.69 2.85
3718 4642 7.986320 ACTAGAGTAGTGATCTAAACGCTCTTA 59.014 37.037 13.02 4.45 37.69 2.10
3719 4643 7.811117 AGAGTAGTGATCTAAACGCTCTTAT 57.189 36.000 0.00 0.00 33.87 1.73
3720 4644 8.905660 AGAGTAGTGATCTAAACGCTCTTATA 57.094 34.615 0.00 0.00 33.87 0.98
3721 4645 9.509956 AGAGTAGTGATCTAAACGCTCTTATAT 57.490 33.333 0.00 0.00 33.87 0.86
3731 4655 9.731819 TCTAAACGCTCTTATATTAGTTCACAG 57.268 33.333 0.00 0.00 0.00 3.66
3732 4656 9.731819 CTAAACGCTCTTATATTAGTTCACAGA 57.268 33.333 0.00 0.00 0.00 3.41
3733 4657 8.635877 AAACGCTCTTATATTAGTTCACAGAG 57.364 34.615 0.00 0.00 0.00 3.35
3734 4658 7.569639 ACGCTCTTATATTAGTTCACAGAGA 57.430 36.000 0.00 0.00 0.00 3.10
3735 4659 7.644490 ACGCTCTTATATTAGTTCACAGAGAG 58.356 38.462 0.00 0.00 34.15 3.20
3736 4660 7.499563 ACGCTCTTATATTAGTTCACAGAGAGA 59.500 37.037 4.35 0.00 32.80 3.10
3737 4661 8.015087 CGCTCTTATATTAGTTCACAGAGAGAG 58.985 40.741 0.00 0.00 30.76 3.20
3786 4723 8.592155 TCAGAAGATATATGTTTTCGTTTCACG 58.408 33.333 0.00 0.00 44.19 4.35
3825 4780 6.071616 GGCACCACTTGGAAAATTCTTATGTA 60.072 38.462 1.14 0.00 38.94 2.29
3827 4782 7.312899 CACCACTTGGAAAATTCTTATGTACC 58.687 38.462 1.14 0.00 38.94 3.34
3833 4788 9.410556 CTTGGAAAATTCTTATGTACCAAGTTG 57.589 33.333 0.00 0.00 44.28 3.16
3852 5123 8.019669 CCAAGTTGATGTAGAAATCTGAAACAG 58.980 37.037 3.87 0.00 0.00 3.16
3868 5139 7.907389 TCTGAAACAGGTGACAATATTACTCT 58.093 34.615 0.00 0.00 31.51 3.24
3883 5154 9.769093 CAATATTACTCTTTTGTTAGTTTCCGG 57.231 33.333 0.00 0.00 0.00 5.14
3905 5176 1.307355 TGCACCGCTGGAATGTCATG 61.307 55.000 1.50 0.00 0.00 3.07
3955 5227 2.555757 GGCCTGCTTGGAATGTCATATC 59.444 50.000 0.00 0.00 38.35 1.63
3987 5259 0.250597 ACCTGTAAAACACCCTCCGC 60.251 55.000 0.00 0.00 0.00 5.54
4004 5276 2.335712 GCAAAGAGAACTGGGCGGG 61.336 63.158 0.00 0.00 0.00 6.13
4005 5277 2.034221 AAAGAGAACTGGGCGGGC 59.966 61.111 0.00 0.00 0.00 6.13
4006 5278 2.529744 AAAGAGAACTGGGCGGGCT 61.530 57.895 0.26 0.00 0.00 5.19
4007 5279 2.069165 AAAGAGAACTGGGCGGGCTT 62.069 55.000 0.26 0.00 0.00 4.35
4008 5280 2.034221 GAGAACTGGGCGGGCTTT 59.966 61.111 0.26 0.00 0.00 3.51
4009 5281 1.603739 GAGAACTGGGCGGGCTTTT 60.604 57.895 0.26 0.00 0.00 2.27
4010 5282 1.152546 AGAACTGGGCGGGCTTTTT 60.153 52.632 0.26 0.00 0.00 1.94
4011 5283 1.179174 AGAACTGGGCGGGCTTTTTC 61.179 55.000 0.26 1.86 0.00 2.29
4012 5284 1.152546 AACTGGGCGGGCTTTTTCT 60.153 52.632 0.26 0.00 0.00 2.52
4013 5285 0.111639 AACTGGGCGGGCTTTTTCTA 59.888 50.000 0.26 0.00 0.00 2.10
4015 5287 1.253100 CTGGGCGGGCTTTTTCTAAA 58.747 50.000 0.26 0.00 0.00 1.85
4016 5288 1.616374 CTGGGCGGGCTTTTTCTAAAA 59.384 47.619 0.26 0.00 0.00 1.52
4018 5290 2.232696 TGGGCGGGCTTTTTCTAAAATC 59.767 45.455 0.26 0.00 0.00 2.17
4019 5291 2.496070 GGGCGGGCTTTTTCTAAAATCT 59.504 45.455 0.26 0.00 0.00 2.40
4020 5292 3.697542 GGGCGGGCTTTTTCTAAAATCTA 59.302 43.478 0.26 0.00 0.00 1.98
4021 5293 4.158949 GGGCGGGCTTTTTCTAAAATCTAA 59.841 41.667 0.26 0.00 0.00 2.10
4023 5295 6.338146 GGCGGGCTTTTTCTAAAATCTAAAT 58.662 36.000 0.00 0.00 0.00 1.40
4024 5296 6.255670 GGCGGGCTTTTTCTAAAATCTAAATG 59.744 38.462 0.00 0.00 0.00 2.32
4025 5297 6.237835 GCGGGCTTTTTCTAAAATCTAAATGC 60.238 38.462 0.00 0.00 32.85 3.56
4026 5298 6.811170 CGGGCTTTTTCTAAAATCTAAATGCA 59.189 34.615 0.00 0.00 34.33 3.96
4027 5299 7.330700 CGGGCTTTTTCTAAAATCTAAATGCAA 59.669 33.333 0.00 0.00 34.33 4.08
4055 5337 1.742761 AGATCGGCCACAAGATGTTG 58.257 50.000 2.24 0.13 39.82 3.33
4056 5338 0.099436 GATCGGCCACAAGATGTTGC 59.901 55.000 2.24 0.00 38.19 4.17
4057 5339 0.608856 ATCGGCCACAAGATGTTGCA 60.609 50.000 2.24 0.00 40.38 4.08
4058 5340 1.210931 CGGCCACAAGATGTTGCAG 59.789 57.895 2.24 1.31 40.38 4.41
4059 5341 1.236616 CGGCCACAAGATGTTGCAGA 61.237 55.000 2.24 0.00 40.38 4.26
4060 5342 0.961019 GGCCACAAGATGTTGCAGAA 59.039 50.000 1.83 0.00 40.38 3.02
4061 5343 1.068055 GGCCACAAGATGTTGCAGAAG 60.068 52.381 1.83 0.00 40.38 2.85
4062 5344 1.881973 GCCACAAGATGTTGCAGAAGA 59.118 47.619 1.83 0.00 38.70 2.87
4063 5345 2.095364 GCCACAAGATGTTGCAGAAGAG 60.095 50.000 1.83 0.00 38.70 2.85
4064 5346 2.095364 CCACAAGATGTTGCAGAAGAGC 60.095 50.000 1.83 0.00 37.14 4.09
4065 5347 2.812591 CACAAGATGTTGCAGAAGAGCT 59.187 45.455 1.83 0.00 37.14 4.09
4066 5348 3.252701 CACAAGATGTTGCAGAAGAGCTT 59.747 43.478 1.83 0.00 37.14 3.74
4067 5349 3.822996 CAAGATGTTGCAGAAGAGCTTG 58.177 45.455 0.00 0.00 40.96 4.01
4068 5350 1.811359 AGATGTTGCAGAAGAGCTTGC 59.189 47.619 1.00 1.00 34.99 4.01
4069 5351 1.811359 GATGTTGCAGAAGAGCTTGCT 59.189 47.619 9.40 0.00 34.99 3.91
4070 5352 2.549064 TGTTGCAGAAGAGCTTGCTA 57.451 45.000 9.40 0.00 34.99 3.49
4071 5353 2.849942 TGTTGCAGAAGAGCTTGCTAA 58.150 42.857 9.40 0.48 34.99 3.09
4072 5354 2.810274 TGTTGCAGAAGAGCTTGCTAAG 59.190 45.455 9.40 0.00 34.99 2.18
4086 5368 5.886960 CTTGCTAAGCACAGTAAAATCCT 57.113 39.130 0.00 0.00 38.71 3.24
4087 5369 5.873732 CTTGCTAAGCACAGTAAAATCCTC 58.126 41.667 0.00 0.00 38.71 3.71
4088 5370 5.165961 TGCTAAGCACAGTAAAATCCTCT 57.834 39.130 0.00 0.00 31.71 3.69
4089 5371 5.560724 TGCTAAGCACAGTAAAATCCTCTT 58.439 37.500 0.00 0.00 31.71 2.85
4090 5372 6.003950 TGCTAAGCACAGTAAAATCCTCTTT 58.996 36.000 0.00 0.00 31.71 2.52
4091 5373 6.072508 TGCTAAGCACAGTAAAATCCTCTTTG 60.073 38.462 0.00 0.00 31.71 2.77
4109 5391 6.183360 CCTCTTTGTGTACATTCGGATTACAC 60.183 42.308 16.18 16.18 43.91 2.90
4114 5396 5.047590 TGTGTACATTCGGATTACACTGTCT 60.048 40.000 20.32 0.00 43.96 3.41
4118 5400 3.394674 TTCGGATTACACTGTCTGCAA 57.605 42.857 0.00 0.00 0.00 4.08
4120 5402 3.734463 TCGGATTACACTGTCTGCAAAA 58.266 40.909 0.00 0.00 0.00 2.44
4123 5405 4.213270 CGGATTACACTGTCTGCAAAAAGA 59.787 41.667 0.00 0.00 0.00 2.52
4124 5406 5.277779 CGGATTACACTGTCTGCAAAAAGAA 60.278 40.000 0.00 0.00 0.00 2.52
4125 5407 6.568462 CGGATTACACTGTCTGCAAAAAGAAT 60.568 38.462 0.00 0.00 0.00 2.40
4126 5408 7.147976 GGATTACACTGTCTGCAAAAAGAATT 58.852 34.615 0.00 0.00 0.00 2.17
4127 5409 8.296713 GGATTACACTGTCTGCAAAAAGAATTA 58.703 33.333 0.00 0.00 0.00 1.40
4128 5410 9.677567 GATTACACTGTCTGCAAAAAGAATTAA 57.322 29.630 0.00 0.00 0.00 1.40
4129 5411 9.683069 ATTACACTGTCTGCAAAAAGAATTAAG 57.317 29.630 0.00 0.00 0.00 1.85
4131 5413 5.978919 CACTGTCTGCAAAAAGAATTAAGCA 59.021 36.000 0.00 0.00 0.00 3.91
4132 5414 6.643770 CACTGTCTGCAAAAAGAATTAAGCAT 59.356 34.615 0.00 0.00 30.94 3.79
4134 5416 8.025445 ACTGTCTGCAAAAAGAATTAAGCATAG 58.975 33.333 0.00 0.00 30.94 2.23
4154 5524 8.957466 AGCATAGAATTTTGTTTTAGGTACTCC 58.043 33.333 0.00 0.00 41.75 3.85
4162 5532 8.584063 TTTTGTTTTAGGTACTCCTTCAGTTT 57.416 30.769 0.00 0.00 42.12 2.66
4172 5542 3.182967 CTCCTTCAGTTTAGCTAGTGCG 58.817 50.000 0.00 0.00 45.42 5.34
4194 5564 3.791973 AACAGACGACAGATCATCCTC 57.208 47.619 0.00 0.00 0.00 3.71
4195 5565 2.028130 ACAGACGACAGATCATCCTCC 58.972 52.381 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.932710 GGTTAAGATGCGACTTGTGATCA 59.067 43.478 0.00 0.00 0.00 2.92
54 55 2.645838 AGACAACAGCAGAACATGGT 57.354 45.000 0.00 0.00 41.36 3.55
56 57 3.120408 GCACTAGACAACAGCAGAACATG 60.120 47.826 0.00 0.00 0.00 3.21
67 68 7.716768 AGAAAAGAAACTAGCACTAGACAAC 57.283 36.000 11.59 1.06 36.97 3.32
93 94 4.792068 ACAAATGAGGGAGTGAGACAAAA 58.208 39.130 0.00 0.00 0.00 2.44
99 100 5.128499 ACTGATCTACAAATGAGGGAGTGAG 59.872 44.000 0.00 0.00 0.00 3.51
102 103 4.407296 GGACTGATCTACAAATGAGGGAGT 59.593 45.833 0.00 0.00 0.00 3.85
140 141 1.949631 GGATCTTACGAAGCGGCCG 60.950 63.158 24.05 24.05 0.00 6.13
145 146 2.510768 ATCGGTGGATCTTACGAAGC 57.489 50.000 9.45 0.00 38.94 3.86
166 167 2.203552 TCAAACATGCCGGGCCAA 60.204 55.556 17.97 0.00 0.00 4.52
169 170 2.490993 CTTGGTCAAACATGCCGGGC 62.491 60.000 13.32 13.32 0.00 6.13
171 172 0.673437 AACTTGGTCAAACATGCCGG 59.327 50.000 0.00 0.00 0.00 6.13
173 174 3.740832 GCTAAAACTTGGTCAAACATGCC 59.259 43.478 0.00 0.00 0.00 4.40
175 176 4.445385 GCAGCTAAAACTTGGTCAAACATG 59.555 41.667 0.00 0.00 0.00 3.21
204 205 4.746702 GCCAGCAACTATCCCTAAAGCATA 60.747 45.833 0.00 0.00 0.00 3.14
214 215 1.369091 CCACGTGCCAGCAACTATCC 61.369 60.000 10.91 0.00 0.00 2.59
233 234 2.350772 CGTTTTTCCACATCTGGCAGTC 60.351 50.000 15.27 0.00 37.49 3.51
252 253 8.120140 ACTACCTAGTTATTTGTCTTCTTCGT 57.880 34.615 0.00 0.00 31.13 3.85
261 262 9.813446 GCAAGTACATACTACCTAGTTATTTGT 57.187 33.333 0.00 0.00 37.73 2.83
262 263 9.811995 TGCAAGTACATACTACCTAGTTATTTG 57.188 33.333 0.00 0.00 37.73 2.32
266 267 7.977853 GCTTTGCAAGTACATACTACCTAGTTA 59.022 37.037 0.00 0.00 37.73 2.24
267 268 6.817140 GCTTTGCAAGTACATACTACCTAGTT 59.183 38.462 0.00 0.00 37.73 2.24
268 269 6.070995 TGCTTTGCAAGTACATACTACCTAGT 60.071 38.462 0.00 0.00 36.57 2.57
269 270 6.338146 TGCTTTGCAAGTACATACTACCTAG 58.662 40.000 0.00 0.00 34.76 3.02
270 271 6.288941 TGCTTTGCAAGTACATACTACCTA 57.711 37.500 0.00 0.00 34.76 3.08
271 272 5.160607 TGCTTTGCAAGTACATACTACCT 57.839 39.130 0.00 0.00 34.76 3.08
272 273 4.332819 CCTGCTTTGCAAGTACATACTACC 59.667 45.833 0.00 0.00 38.41 3.18
273 274 4.935808 ACCTGCTTTGCAAGTACATACTAC 59.064 41.667 0.00 0.00 38.41 2.73
289 290 2.641815 AGACCAAGATCTGAACCTGCTT 59.358 45.455 0.00 0.00 0.00 3.91
291 292 2.777832 AGACCAAGATCTGAACCTGC 57.222 50.000 0.00 0.00 0.00 4.85
297 298 8.774546 ATGATACTTTCTAGACCAAGATCTGA 57.225 34.615 10.51 0.00 0.00 3.27
348 349 2.148916 TAACAGACAGGAACGTGCAG 57.851 50.000 0.00 0.00 0.00 4.41
385 386 7.257722 ACTGTAAAAACATTTTCACTGACAGG 58.742 34.615 7.51 0.00 35.90 4.00
416 417 9.613428 TCCTATCAAACCACAATATAACAGAAG 57.387 33.333 0.00 0.00 0.00 2.85
448 449 6.770303 TGCATCGAGGTAAATTTGGATATTCA 59.230 34.615 0.00 0.00 0.00 2.57
456 457 5.049818 GGAGAGATGCATCGAGGTAAATTTG 60.050 44.000 20.67 0.00 0.00 2.32
475 476 1.293498 CGAACCACACAGGGGAGAG 59.707 63.158 0.00 0.00 43.89 3.20
476 477 2.879233 GCGAACCACACAGGGGAGA 61.879 63.158 0.00 0.00 43.89 3.71
491 492 1.064803 ACAACATGCGTTTTCAAGCGA 59.935 42.857 0.00 0.00 34.38 4.93
513 523 4.379652 ACAACAAAACATTGGAATGGAGC 58.620 39.130 4.45 0.00 40.70 4.70
569 579 2.768253 TCCAGTGTCATTTCGCATCT 57.232 45.000 0.00 0.00 0.00 2.90
574 584 2.350804 CAGAGCATCCAGTGTCATTTCG 59.649 50.000 0.00 0.00 33.66 3.46
580 590 2.093816 TCATGACAGAGCATCCAGTGTC 60.094 50.000 0.00 0.00 39.85 3.67
583 593 2.168106 GAGTCATGACAGAGCATCCAGT 59.832 50.000 27.02 1.97 33.66 4.00
621 631 5.169561 CGCACAATTGTACAAATATCGAAGC 59.830 40.000 13.23 4.77 0.00 3.86
631 641 4.576216 ATTGGTTCGCACAATTGTACAA 57.424 36.364 11.53 11.41 35.11 2.41
636 646 7.741216 CAGAAAAATAATTGGTTCGCACAATTG 59.259 33.333 16.67 3.24 45.29 2.32
637 647 7.571059 GCAGAAAAATAATTGGTTCGCACAATT 60.571 33.333 13.53 13.53 46.76 2.32
639 649 5.176590 GCAGAAAAATAATTGGTTCGCACAA 59.823 36.000 0.00 0.00 0.00 3.33
644 654 4.922692 TGCTGCAGAAAAATAATTGGTTCG 59.077 37.500 20.43 0.00 0.00 3.95
659 669 2.479389 CCGTCTTTTTGTTTGCTGCAGA 60.479 45.455 20.43 0.00 0.00 4.26
664 674 4.111916 CACATTCCGTCTTTTTGTTTGCT 58.888 39.130 0.00 0.00 0.00 3.91
677 687 1.237285 GCAAGACAGGCACATTCCGT 61.237 55.000 0.00 0.00 0.00 4.69
682 692 1.171308 GTCATGCAAGACAGGCACAT 58.829 50.000 16.82 0.00 45.23 3.21
721 731 8.082242 CGAAAGTAAAACTCTGGGAATTTCAAT 58.918 33.333 0.00 0.00 0.00 2.57
724 734 7.198306 TCGAAAGTAAAACTCTGGGAATTTC 57.802 36.000 0.00 0.00 0.00 2.17
735 745 5.608449 ACTACCAAGCTCGAAAGTAAAACT 58.392 37.500 0.00 0.00 0.00 2.66
742 752 3.040147 TCCAACTACCAAGCTCGAAAG 57.960 47.619 0.00 0.00 0.00 2.62
746 756 2.544685 CTGATCCAACTACCAAGCTCG 58.455 52.381 0.00 0.00 0.00 5.03
766 776 2.450609 TTCTCGTAAACCAGAGTGCC 57.549 50.000 0.00 0.00 36.03 5.01
769 779 5.721232 CACCTATTTCTCGTAAACCAGAGT 58.279 41.667 0.00 0.00 36.03 3.24
775 785 3.933332 AGCTGCACCTATTTCTCGTAAAC 59.067 43.478 1.02 0.00 0.00 2.01
777 787 3.887621 AGCTGCACCTATTTCTCGTAA 57.112 42.857 1.02 0.00 0.00 3.18
780 790 1.936547 GGAAGCTGCACCTATTTCTCG 59.063 52.381 1.02 0.00 0.00 4.04
790 800 3.947834 ACTACATAAATGGGAAGCTGCAC 59.052 43.478 1.02 0.00 0.00 4.57
796 806 8.265055 TCTTAAGGTCACTACATAAATGGGAAG 58.735 37.037 1.85 0.00 0.00 3.46
819 829 4.830573 GGCCAGTTTCAGCCTCTT 57.169 55.556 0.00 0.00 46.14 2.85
829 839 1.062488 ACAGACCAGGAAGGCCAGTT 61.062 55.000 5.01 0.00 43.14 3.16
850 860 3.846588 AGCTCCCCTGTAGAAAGAATTCA 59.153 43.478 8.44 0.00 38.06 2.57
851 861 4.495690 AGCTCCCCTGTAGAAAGAATTC 57.504 45.455 0.00 0.00 35.70 2.17
969 979 8.251026 CAGACAAGGTACAGTTTATGATACAGA 58.749 37.037 0.00 0.00 0.00 3.41
982 992 7.979444 TTTAAAAGGATCAGACAAGGTACAG 57.021 36.000 0.00 0.00 0.00 2.74
1005 1015 9.654663 GAAATCCTGTTGTACAAGTAGAGTATT 57.345 33.333 8.98 8.29 0.00 1.89
1044 1054 1.140052 TGTAGGGTGTCGCCATATTGG 59.860 52.381 4.48 0.00 41.55 3.16
1212 1222 1.940613 ACTTGAAGTTTGGTGACGAGC 59.059 47.619 0.00 0.00 0.00 5.03
1345 1355 5.772825 TCTTGGTGAATTCAAAGGAGTTG 57.227 39.130 10.35 0.00 38.71 3.16
1378 1388 4.092091 GCTTCAAGAAGAACATGAGTACCG 59.908 45.833 13.70 0.00 40.79 4.02
1591 1601 0.042131 TTCCCCGGGTAGTGATGACT 59.958 55.000 21.85 0.00 36.07 3.41
2165 2175 1.064952 CAAACGCGTTTGGGAAGAACT 59.935 47.619 42.59 16.94 44.47 3.01
2179 2189 2.755836 TCAAGAACTTGAGCAAACGC 57.244 45.000 12.40 0.00 43.90 4.84
2230 2240 3.861689 GCTTCTCACATATTTTGCCAAGC 59.138 43.478 0.00 0.00 0.00 4.01
2272 2282 1.142060 TCTTCCAAGCGACCTTTTCCA 59.858 47.619 0.00 0.00 0.00 3.53
2401 2411 3.255969 ACATTGGTACGTATGGTGTCC 57.744 47.619 0.00 0.00 0.00 4.02
2476 2486 0.322456 TGCACCCAGTGGCATAGTTC 60.322 55.000 2.61 0.00 34.58 3.01
2612 2622 9.360093 CTAACAAAGTAGTCATTACAGAAGAGG 57.640 37.037 0.00 0.00 34.56 3.69
2689 2703 6.774656 ACAAATGATCAGAAGTTTCTTCCAGT 59.225 34.615 0.09 0.00 34.74 4.00
2690 2704 7.211966 ACAAATGATCAGAAGTTTCTTCCAG 57.788 36.000 0.09 0.88 34.74 3.86
2713 2727 2.353610 CCTGCATTGCCCAGGGAAC 61.354 63.158 10.89 0.00 44.87 3.62
2722 2736 0.674895 AGTTCCTCGACCTGCATTGC 60.675 55.000 0.46 0.46 0.00 3.56
2754 2768 1.670967 CGCAGAGTGCAGACATTCTCA 60.671 52.381 0.00 0.00 45.36 3.27
2787 2801 4.985409 GGATTGTTGAGGTCAGACGATATC 59.015 45.833 0.00 0.00 0.00 1.63
3045 3122 1.069022 CGAGGTGCAACAATGACCTTG 60.069 52.381 3.64 0.00 39.98 3.61
3235 3331 2.000447 GCTGTGACGAATGGTTCCTAC 59.000 52.381 0.00 0.00 0.00 3.18
3268 3364 5.229921 ACGCTGCAAATATCGTAAAACAT 57.770 34.783 0.00 0.00 33.02 2.71
3269 3365 4.671880 ACGCTGCAAATATCGTAAAACA 57.328 36.364 0.00 0.00 33.02 2.83
3270 3366 6.646636 AGATACGCTGCAAATATCGTAAAAC 58.353 36.000 0.00 5.07 40.19 2.43
3274 3370 5.154222 CAGAGATACGCTGCAAATATCGTA 58.846 41.667 0.00 7.09 40.89 3.43
3275 3371 3.983988 CAGAGATACGCTGCAAATATCGT 59.016 43.478 0.00 0.00 38.75 3.73
3276 3372 3.983988 ACAGAGATACGCTGCAAATATCG 59.016 43.478 0.00 0.00 34.73 2.92
3277 3373 5.914085 AACAGAGATACGCTGCAAATATC 57.086 39.130 0.00 4.13 34.73 1.63
3278 3374 8.523658 TCTATAACAGAGATACGCTGCAAATAT 58.476 33.333 0.00 0.00 34.73 1.28
3279 3375 7.882179 TCTATAACAGAGATACGCTGCAAATA 58.118 34.615 0.00 0.00 34.73 1.40
3280 3376 6.749139 TCTATAACAGAGATACGCTGCAAAT 58.251 36.000 0.00 0.00 34.73 2.32
3312 4107 7.094377 ACTGCCAAATGTATAGTTCAAACGATT 60.094 33.333 0.00 0.00 0.00 3.34
3474 4302 7.995463 TGTGAACTTAAACAGTTAAAATGCC 57.005 32.000 0.00 0.00 46.53 4.40
3493 4321 4.036734 AGCAAAGCGAGAGAAAAATGTGAA 59.963 37.500 0.00 0.00 0.00 3.18
3495 4323 3.893720 AGCAAAGCGAGAGAAAAATGTG 58.106 40.909 0.00 0.00 0.00 3.21
3574 4407 5.702670 TCCTCTTTGCTCTGTGAATAACAAG 59.297 40.000 0.00 0.00 38.67 3.16
3575 4408 5.620206 TCCTCTTTGCTCTGTGAATAACAA 58.380 37.500 0.00 0.00 38.67 2.83
3576 4409 5.227569 TCCTCTTTGCTCTGTGAATAACA 57.772 39.130 0.00 0.00 37.22 2.41
3582 4423 1.417517 TGCTTCCTCTTTGCTCTGTGA 59.582 47.619 0.00 0.00 0.00 3.58
3677 4601 9.411189 CACTACTCTAGTATTCTAAACCCTCTT 57.589 37.037 0.00 0.00 37.23 2.85
3680 4604 9.577222 GATCACTACTCTAGTATTCTAAACCCT 57.423 37.037 0.00 0.00 37.23 4.34
3681 4605 9.577222 AGATCACTACTCTAGTATTCTAAACCC 57.423 37.037 0.00 0.00 37.23 4.11
3687 4611 8.776470 GCGTTTAGATCACTACTCTAGTATTCT 58.224 37.037 0.00 0.00 37.23 2.40
3688 4612 8.776470 AGCGTTTAGATCACTACTCTAGTATTC 58.224 37.037 0.00 0.00 37.23 1.75
3689 4613 8.680039 AGCGTTTAGATCACTACTCTAGTATT 57.320 34.615 0.00 0.00 37.23 1.89
3690 4614 8.152246 AGAGCGTTTAGATCACTACTCTAGTAT 58.848 37.037 0.00 0.00 37.82 2.12
3692 4616 6.350906 AGAGCGTTTAGATCACTACTCTAGT 58.649 40.000 0.00 0.00 37.82 2.57
3693 4617 6.854496 AGAGCGTTTAGATCACTACTCTAG 57.146 41.667 0.00 0.00 37.82 2.43
3695 4619 7.811117 ATAAGAGCGTTTAGATCACTACTCT 57.189 36.000 0.00 0.00 37.82 3.24
3705 4629 9.731819 CTGTGAACTAATATAAGAGCGTTTAGA 57.268 33.333 0.00 0.00 0.00 2.10
3706 4630 9.731819 TCTGTGAACTAATATAAGAGCGTTTAG 57.268 33.333 0.00 0.00 0.00 1.85
3707 4631 9.731819 CTCTGTGAACTAATATAAGAGCGTTTA 57.268 33.333 0.00 0.00 0.00 2.01
3708 4632 8.467598 TCTCTGTGAACTAATATAAGAGCGTTT 58.532 33.333 0.00 0.00 31.76 3.60
3709 4633 7.997482 TCTCTGTGAACTAATATAAGAGCGTT 58.003 34.615 0.00 0.00 31.76 4.84
3710 4634 7.499563 TCTCTCTGTGAACTAATATAAGAGCGT 59.500 37.037 0.00 0.00 31.76 5.07
3711 4635 7.866729 TCTCTCTGTGAACTAATATAAGAGCG 58.133 38.462 0.00 0.00 31.76 5.03
3712 4636 8.846211 ACTCTCTCTGTGAACTAATATAAGAGC 58.154 37.037 0.00 0.00 31.76 4.09
3717 4641 9.901172 TGTGTACTCTCTCTGTGAACTAATATA 57.099 33.333 0.00 0.00 0.00 0.86
3718 4642 8.809468 TGTGTACTCTCTCTGTGAACTAATAT 57.191 34.615 0.00 0.00 0.00 1.28
3719 4643 7.883833 ACTGTGTACTCTCTCTGTGAACTAATA 59.116 37.037 0.00 0.00 0.00 0.98
3720 4644 6.717540 ACTGTGTACTCTCTCTGTGAACTAAT 59.282 38.462 0.00 0.00 0.00 1.73
3721 4645 6.062749 ACTGTGTACTCTCTCTGTGAACTAA 58.937 40.000 0.00 0.00 0.00 2.24
3722 4646 5.622180 ACTGTGTACTCTCTCTGTGAACTA 58.378 41.667 0.00 0.00 0.00 2.24
3723 4647 4.465886 ACTGTGTACTCTCTCTGTGAACT 58.534 43.478 0.00 0.00 0.00 3.01
3724 4648 4.839668 ACTGTGTACTCTCTCTGTGAAC 57.160 45.455 0.00 0.00 0.00 3.18
3725 4649 8.809468 ATAATACTGTGTACTCTCTCTGTGAA 57.191 34.615 0.00 0.00 0.00 3.18
3726 4650 8.678199 CAATAATACTGTGTACTCTCTCTGTGA 58.322 37.037 0.00 0.00 0.00 3.58
3727 4651 7.918033 CCAATAATACTGTGTACTCTCTCTGTG 59.082 40.741 0.00 0.00 0.00 3.66
3728 4652 7.616150 ACCAATAATACTGTGTACTCTCTCTGT 59.384 37.037 0.00 0.00 0.00 3.41
3729 4653 8.001881 ACCAATAATACTGTGTACTCTCTCTG 57.998 38.462 0.00 0.00 0.00 3.35
3730 4654 8.596781 AACCAATAATACTGTGTACTCTCTCT 57.403 34.615 0.00 0.00 0.00 3.10
3731 4655 9.303537 GAAACCAATAATACTGTGTACTCTCTC 57.696 37.037 0.00 0.00 0.00 3.20
3732 4656 9.036980 AGAAACCAATAATACTGTGTACTCTCT 57.963 33.333 0.00 0.00 0.00 3.10
3733 4657 9.654663 AAGAAACCAATAATACTGTGTACTCTC 57.345 33.333 0.00 0.00 0.00 3.20
3736 4660 9.787435 TGAAAGAAACCAATAATACTGTGTACT 57.213 29.630 0.00 0.00 0.00 2.73
3825 4780 7.502226 TGTTTCAGATTTCTACATCAACTTGGT 59.498 33.333 0.00 0.00 0.00 3.67
3827 4782 8.019669 CCTGTTTCAGATTTCTACATCAACTTG 58.980 37.037 0.00 0.00 32.44 3.16
3830 4785 7.173218 TCACCTGTTTCAGATTTCTACATCAAC 59.827 37.037 0.00 0.00 32.44 3.18
3833 4788 6.650807 TGTCACCTGTTTCAGATTTCTACATC 59.349 38.462 0.00 0.00 32.44 3.06
3868 5139 3.065648 GTGCAGACCGGAAACTAACAAAA 59.934 43.478 9.46 0.00 0.00 2.44
3883 5154 1.639298 GACATTCCAGCGGTGCAGAC 61.639 60.000 9.63 0.00 0.00 3.51
3955 5227 0.916086 TACAGGTGTATTGGGCTGGG 59.084 55.000 0.00 0.00 0.00 4.45
3987 5259 2.335712 GCCCGCCCAGTTCTCTTTG 61.336 63.158 0.00 0.00 0.00 2.77
4025 5297 1.009829 GGCCGATCTTGCAGTAGTTG 58.990 55.000 6.45 0.00 0.00 3.16
4026 5298 0.613260 TGGCCGATCTTGCAGTAGTT 59.387 50.000 0.00 0.00 0.00 2.24
4027 5299 0.108138 GTGGCCGATCTTGCAGTAGT 60.108 55.000 0.00 0.00 0.00 2.73
4030 5302 0.957395 CTTGTGGCCGATCTTGCAGT 60.957 55.000 0.00 0.00 0.00 4.40
4031 5303 0.674581 TCTTGTGGCCGATCTTGCAG 60.675 55.000 0.00 0.00 0.00 4.41
4033 5305 0.379669 CATCTTGTGGCCGATCTTGC 59.620 55.000 0.00 0.00 0.00 4.01
4034 5306 1.742761 ACATCTTGTGGCCGATCTTG 58.257 50.000 0.00 0.00 0.00 3.02
4035 5307 2.086869 CAACATCTTGTGGCCGATCTT 58.913 47.619 0.00 0.00 0.00 2.40
4036 5308 1.742761 CAACATCTTGTGGCCGATCT 58.257 50.000 0.00 0.00 0.00 2.75
4064 5346 5.645497 AGAGGATTTTACTGTGCTTAGCAAG 59.355 40.000 9.05 11.24 41.47 4.01
4065 5347 5.560724 AGAGGATTTTACTGTGCTTAGCAA 58.439 37.500 9.05 0.00 41.47 3.91
4066 5348 5.165961 AGAGGATTTTACTGTGCTTAGCA 57.834 39.130 1.39 1.39 35.60 3.49
4067 5349 6.072452 ACAAAGAGGATTTTACTGTGCTTAGC 60.072 38.462 0.00 0.00 0.00 3.09
4068 5350 7.041098 ACACAAAGAGGATTTTACTGTGCTTAG 60.041 37.037 0.00 0.00 0.00 2.18
4069 5351 6.770785 ACACAAAGAGGATTTTACTGTGCTTA 59.229 34.615 0.00 0.00 0.00 3.09
4070 5352 5.594317 ACACAAAGAGGATTTTACTGTGCTT 59.406 36.000 0.00 0.00 0.00 3.91
4071 5353 5.133221 ACACAAAGAGGATTTTACTGTGCT 58.867 37.500 0.00 0.00 0.00 4.40
4072 5354 5.438761 ACACAAAGAGGATTTTACTGTGC 57.561 39.130 0.00 0.00 0.00 4.57
4073 5355 7.490962 TGTACACAAAGAGGATTTTACTGTG 57.509 36.000 0.00 0.00 0.00 3.66
4074 5356 8.691661 AATGTACACAAAGAGGATTTTACTGT 57.308 30.769 0.00 0.00 0.00 3.55
4075 5357 7.957484 CGAATGTACACAAAGAGGATTTTACTG 59.043 37.037 0.00 0.00 0.00 2.74
4076 5358 7.119262 CCGAATGTACACAAAGAGGATTTTACT 59.881 37.037 0.00 0.00 0.00 2.24
4077 5359 7.118680 TCCGAATGTACACAAAGAGGATTTTAC 59.881 37.037 0.00 0.00 0.00 2.01
4078 5360 7.162761 TCCGAATGTACACAAAGAGGATTTTA 58.837 34.615 0.00 0.00 0.00 1.52
4079 5361 6.001460 TCCGAATGTACACAAAGAGGATTTT 58.999 36.000 0.00 0.00 0.00 1.82
4080 5362 5.556915 TCCGAATGTACACAAAGAGGATTT 58.443 37.500 0.00 0.00 0.00 2.17
4081 5363 5.160607 TCCGAATGTACACAAAGAGGATT 57.839 39.130 0.00 0.00 0.00 3.01
4082 5364 4.819105 TCCGAATGTACACAAAGAGGAT 57.181 40.909 0.00 0.00 0.00 3.24
4083 5365 4.819105 ATCCGAATGTACACAAAGAGGA 57.181 40.909 0.00 2.25 0.00 3.71
4084 5366 5.872617 TGTAATCCGAATGTACACAAAGAGG 59.127 40.000 0.00 0.00 0.00 3.69
4085 5367 6.590292 AGTGTAATCCGAATGTACACAAAGAG 59.410 38.462 13.82 0.00 46.52 2.85
4086 5368 6.367695 CAGTGTAATCCGAATGTACACAAAGA 59.632 38.462 13.82 0.00 46.52 2.52
4087 5369 6.147164 ACAGTGTAATCCGAATGTACACAAAG 59.853 38.462 13.82 7.14 46.52 2.77
4088 5370 5.992829 ACAGTGTAATCCGAATGTACACAAA 59.007 36.000 13.82 0.00 46.52 2.83
4089 5371 5.543714 ACAGTGTAATCCGAATGTACACAA 58.456 37.500 13.82 0.00 46.52 3.33
4090 5372 5.047590 AGACAGTGTAATCCGAATGTACACA 60.048 40.000 13.82 0.00 46.52 3.72
4091 5373 5.288712 CAGACAGTGTAATCCGAATGTACAC 59.711 44.000 0.00 5.29 45.15 2.90
4109 5391 8.239314 TCTATGCTTAATTCTTTTTGCAGACAG 58.761 33.333 0.00 0.00 33.87 3.51
4128 5410 8.957466 GGAGTACCTAAAACAAAATTCTATGCT 58.043 33.333 0.00 0.00 0.00 3.79
4129 5411 8.957466 AGGAGTACCTAAAACAAAATTCTATGC 58.043 33.333 0.00 0.00 45.83 3.14
4154 5524 4.947420 GTTTCGCACTAGCTAAACTGAAG 58.053 43.478 9.47 0.00 46.77 3.02
4162 5532 1.808343 TCGTCTGTTTCGCACTAGCTA 59.192 47.619 0.00 0.00 39.10 3.32
4172 5542 4.109050 GAGGATGATCTGTCGTCTGTTTC 58.891 47.826 11.57 0.00 39.77 2.78


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.